DNA as a universal substrate for chemical kinetics

Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions. By using strand displacement reactions as a primitive, we construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously, reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into real chemical systems. We illustrate our method on the Lotka–Volterra oscillator, a limit-cycle oscillator, a chaotic system, and systems implementing feedback digital logic and algorithmic behavior

Quantum Indistinguishability in Chemical Reactions

Quantum indistinguishability plays a crucial role in many low-energy physical phenomena, from quantum fluids to molecular spectroscopy. It is, however, typically ignored in most high temperature processes, particularly for ionic coordinates, implicitly assumed to be distinguishable, incoherent and thus well-approximated classically. We explore chemical reactions involving small symmetric molecules, and argue that in many situations a full quantum treatment of collective nuclear degrees of freedom is essential. Supported by several physical arguments, we conjecture a "Quantum Dynamical Selection" (QDS) rule for small symmetric molecules that precludes chemical processes that involve direct transitions from orbitally non-symmetric molecular states. As we propose and discuss, the implications of the Quantum Dynamical Selection rule include: (i) a differential chemical reactivity of para- and ortho-hydrogen, (ii) a mechanism for inducing inter-molecular quantum entanglement of nuclear spins, (iii) a new isotope fractionation mechanism, (iv) a novel explanation of the enhanced chemical activity of "Reactive Oxygen Species", (v) illuminating the importance of ortho-water molecules in modulating the quantum dynamics of liquid water, (vi) providing the critical quantum-to-biochemical linkage in the nuclear spin model of the (putative) quantum brain, among others.Comment: 12 pages, 5 figures. Clarified presentation and figure

Modeling and simulating chemical reactions

Many students are familiar with the idea of modeling chemical reactions in terms of ordinary differential equations. However, these deterministic reaction rate equations are really a certain large-scale limit of a sequence of finer-scale probabilistic models. In studying this hierarchy of models, students can be exposed to a range of modern ideas in applied and computational mathematics. This article introduces some of the basic concepts in an accessible manner and points to some challenges that currently occupy researchers in this area. Short, downloadable MATLAB codes are listed and described